SLX4IP

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			48 clinvar	4 clinvar		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	50	5	0	55

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001009608.3	RefSeq	NP_001009608.1	7	MANE Select
ENST00000334534.10	Ensembl	ENSP00000335557.5	7	MANE Select
ENST00000488816.1	Ensembl	ENSP00000432784.1	3	Standard
ENST00000931374.1	Ensembl	ENSP00000601433.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334534
Coding exons: 7
Length: 201527
Individuals with no LoFs: 125588
Homozygous LoFs: 1
Heterozygous LoFs: 159
Defined: 125748
p: 0.000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.327	203	217	0.938	0.0000114	2664
Missense (PolyPhen)		45	47.129	0.95483		657
Synonymous	0.343	76	79.9	0.951	0.00000438	779
Loss of Function	-0.0277	18	17.9	1.01	9.21e-7	233

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0019	0.0019	notable
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00028	0.00027	rare
Finnish	0.0033	0.0032	notable
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00036	0.00036	rare
Other	0.00054	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Disease: DISEASE: Note=Chromosomal aberrations involving SLX4IP are found in acute lymphoblastic leukemia. A site-specific deletion within the 5' region of SLX4IP is found in 30% of childhood acute lymphoblastic leukemia in general and more than 60% of ETV6/RUNX1- rearranged acute lymphoblastic leukemia. Breakpoints within SLX4IP reveal junctions with typical characteristics of illegitimate V(D)J mediated recombination. SLX4IP deletions are significantly associated with male gender and ETV6/RUNX1-rearranged acute lymphoblastic leukemia. {ECO:0000269|PubMed:24045615}.;

Recessive Scores

pRec: 0.0573

Intolerance Scores

RVIS EVS: 0.4
RVIS percentile EVS: 76.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium